How could she be so sure baby was Elliot's vs. Tom (or vice versa)?

I don't understand. When she's asked whether the father is Tom, Elizabeth McGovern states: "No, it's Elliott."

Then later Elizabeth McGovern says just as confidently: "It's NOT Elliott's. It's Tom's!"

How would anyone know definitively who the father of their baby is if they slept with two different men within a few days of each other?

I hate stupid plot elements like that!